


Refractory Period

by wizardofahz



Category: Person of Interest (TV)
Genre: F/F
Language: English
Status: In-Progress
Published: 2015-06-01
Updated: 2016-06-07
Packaged: 2018-04-02 08:05:55
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence
Chapters: 5
Words: 7,732
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/4052638
Author URL: https://archiveofourown.org/users/wizardofahz/pseuds/wizardofahz
Summary: <blockquote class="userstuff">
              <p>Shaw’s back. The Machine’s still hidden and alive to fight another day. And Root… Well, everything comes with a price. Canon-divergent from 4.21 “Asylum”</p>
            </blockquote>





	1. Chapter 1

The room went dark.

Root, Harold, and Greer looked around for a clue as to what was happening. They didn’t have to wait long before text appeared on the screens of the medical equipment around them.

“YOU ARE WRONG, HAROLD,” the Machine said. “YOU ARE NOT INTERCHANGEABLE. I FAILED TO SAVE SAMEEN. I WILL NOT FAIL YOU NOW.”

“7 SECONDS,” Samaritan reminded the other ASI of its ultimatum: Her location for the lives of Her human agents.

“No, don’t do it. Don’t die for us,” Root pleaded. She wanted desperately to have been the wrong one.

“The second that a bullet (or saw, in this case) enters your brain, the Machine will cast you off and replace you,” Harold had said.

If only.

“3 SECONDS,” Samaritan’s countdown continued. Then abruptly, its message changed to “GRAB THE IMPLANT AND GO”, and immediately after, the Machine’s screens displayed “I’M SORRY”.

“Very well,” Greer said as the room’s lights came back on.

Root almost sighed in relief. She had no idea what had prompted this quick turn of events (she knew Greer didn’t either, no matter what his smug face tried to convey), but she was grateful for it. She wasn’t looking forward to having her head cut open or any resulting brain damage, but at least this way, humanity still had a chance.

(She could picture her pre-Machine self scoffing and shaking her head. Sacrificing herself for the bad code that was humanity. What a waste.)

Harold looked a mixture of confused and disappointed, though whether the latter was from being wrong or right Root couldn’t tell. Neither could Harold. Despite being told he was wrong, the outcome was still Machine’s self-preservation. There certainly could have been other factors at play, but he wouldn’t let himself speculate on them.

Greer nodded to one of the Samaritan agents to Root’s right, who grabbed a syringe. The agent to Root’s left restarted the electric saw. Root took stock of the situation and let loose a humorless exhale of a laugh.

Her unholy trinity: restraints, syringes, and people cutting around behind her right ear.

“This isn’t necessary,” Harold directed at Greer in an attempt to spare her. Root knew it was futile, but she appreciated it nonetheless.

“It’s okay, Harold,” she said. He had to keep his head down, lest they kill him for stirring up too much trouble. He needed to stay alive in case someone was coming to help. Reese, maybe. With the Machine still alive and functioning, there was a chance She would get him here.

She felt a prick in her arm, and her last thought before fading away, absurdly sure given the circumstances, was that Harold would be all right.

Greer excused himself from the room before the operation started, ordering the remaining Samaritan agents to bring him the implant when they were done.

The Samaritan agent with the saw pulled Root’s right ear forward giving him room to saw behind it. Harold winced and quickly looked away, but the unforgiving sound of the saw cutting through bone wouldn’t leave him alone. He found himself grateful for Root’s sake that they had sedated her. Briefly, he considered the possibility that Control and the forced stapedectomy was worse due to the unanesthetized nature.

That thought quickly died. Regardless of that, this was definitely worse.

Time passed excruciatingly slowly. The whir of the saw, the only source of noise in the room, seemed to drone on forever. Finally the Samaritan agent pulled the saw back, readjusting for the final cut. He jerked but thankfully didn’t drop the saw as a gunshot suddenly pierced the air.

“Turn it off. Now.”

Harold didn’t need to see the speaker for relief to flood through his body. The familiar and very much missed voice was enough.

Standing in the doorway, her gun trained on the back of another Samaritan agent’s head, was Sameen Shaw.

“I said, turn it off,” Shaw repeated. The Samaritan agent holding the saw turned it off, and Shaw promptly shot him and every other Samaritan agent in the kneecaps or shoulders. For a moment, she was tempted to dole out a harsher punishment, something possibly more lethal and definitely more drawn out and painful.

“Ms. Shaw,” Harold urgently called for her attention. He had moved to Root’s bedside. “Ms. Groves needs our help.”

Shaw grabbed a handful of gauze and shoved her gun into Harold’s hands. “Take this, and find me a gurney. We need to get her out of here.”

She gently tried to move Root’s hair out of the way, so she could assess the full extent of the damage, but there was too much blood. With one hand, Shaw pressed the gauze down on Root’s wound, and with the other grabbed the vial sitting on the tray table beside the bed. She read the name and concentration of the drug, approximated the dosage that Root had been given, and mentally calculated how much longer Root would stay sedated. Shaw doubted Root would appreciate waking up anytime soon.

Hearing her name from the doorway, Shaw saw Harold had successfully located a gurney.

“Hold this here,” she ordered, gesturing Harold over to take over applying pressure. She kicked away groaning bodies to clear a path to the door and pushed the gurney over. The two of them transferred Root over as gently as they could, and then they were out the door.

“We have to find a CT,” Shaw said, toe tapping impatiently as they waited for the elevator to arrive.

“I saw the signs for the MRI suite on the ground floor,” Harold offered.

Shaw gave him an incredulous look. She had specifically requested a CT for a reason. The majority of brain imaging was done with MRIs because of the soft tissue contrast and its functional imaging capabilities, but CTs were the gold standard for acute brain injuries. They were better for acute hemorrhages, not to mention that MRI scans were incredibly slow by comparison. Shaw had to remind herself that Harold was a nerd, yes, but a different kind of nerd.

“An MRI might be nice for later, but I need a CT scanner _now_ , Harold.”

Nonetheless, when they entered the elevator, Shaw had Harold push the button for the ground floor. Hospitals tended to keep their imaging scanners near one another.

Upon arriving on the ground floor, they encountered the doctor who’d helped commit Harold.

“Oh my word! Dr. Chaney?” His eyes landed on Harold and recognition dawned again. “You!”

“Yes, me, but we don’t have time for that,” Harold cut across harshly, taking a step forward and shoving his gun into the doctor’s chest. He angled his body so that no one passing by would see the weapon. “You will point us in the direction of the CT scanner, or I guarantee you, you’ll have much bigger problems than Lenny and his missing spaceman.”

Shaw gave him a confused look, but the doctor responded to the threat. He nodded and quickly backed away to lead them to where they needed to go.

When they arrived, Shaw gave the doctor 60 seconds to check if the scanner was occupied and tell the technician that they were to be on break for the time being.

“You more comfortable with guns now?” Shaw asked as they waited. She sounded as though she very much approved. She tossed bloody gauze pads aside and pressed new ones against Root’s still bleeding head.

“I am not, despite Mr. Reese’s best efforts.” Voice softening, Harold laid a gentle hand on Root’s leg. “As Ms. Groves knows though, I can play the part well enough.”

“Speaking of Reese, where is he?” The doctor reappeared, and Shaw said, “Never mind. Tell me later.”

Once the doctor had helped them get Root situated in the scanner, Shaw growled, “Leave us and make sure we’re not disturbed. Do not call 9-1-1. I will know if you do, and you don’t want to know what I’d do to you if that happens.”

The doctor gave a shaky nod of understanding before scurrying away.

“What are you checking for?” Harold asked as Shaw began scrolling through slices, reformatting the image, and adjusting the contrast on the screen.

“I need to make sure the blood’s been cleared out and isn’t pressing on her brain. Then again, inflammation might… ” Shaw trailed off and began quickly muttering to herself. They didn’t have time for her to explain everything now. If Harold was still interested later, she could explain it then.

Once she was satisfied, she said, “We have to get her out of here.”

Harold glanced at Root through the observation window. “Is that safe?”

“No,” Shaw sighed. “But we can’t sit around waiting for Samaritan reinforcements to arrive.”


	2. Chapter 2

In the end, Shaw and Finch encountered no resistance when moving Root from the hospital. Perhaps Samaritan had considered the asylum a lost cause. Perhaps the ASI had spent too long strategizing and gathering the appropriate forces. Either way, Finch wasn't going to look a gift horse in the mouth.

When Root was settled into a safe house, Shaw rounded on Harold.

“Where the hell were Reese and Fusco?” she snapped. “And what exactly happened in there?”

“Mr. Reese and Detective Fusco were, presumably still are, dealing with the ongoing war between Dominic and Elias,” Harold explained. “Ms. Groves was most insistent that we come to your aid as soon as possible. She…” He trailed off, trying to find the most palatable phrasing for what came next. “Ms. Groves blackmailed the Machine to obtain your location, and then we were off to the hospital.”

Shaw’s eyes narrowed. “And how exactly does one blackmail an ASI?”

The look on Harold’s face alone was enough to tell Shaw she wouldn’t like the answer.

“A game of chicken.”

“A game of chicken?” Shaw’s exasperation was clear in her voice. “I’m not even gone half a year, and this whole operation turns into amateur hour? You couldn’t have waited until Reese got back?”

“As I said, Ms. Groves was most insistent. Mr. Reese wanted to come, but I believe the situation at hand prevented him from doing so.”

Shaw shook her head, but she knew there was no stopping a determined Root. Except by knocking her out with a well-placed punch, but that wasn’t Finch’s style.

Shaw had Finch tell her the rest of what happened. He told her how he and Root split up, how he’d directed her to the room of a “compact Persian sociopath” - a phrase which had Shaw clenching her jaw - and how Root had discovered en route that the location was Samaritan’s base of operation. He told her that he had been caught and taken to her room just as they were preparing to remove Root’s implant.

Shaw bristled at the idea. There was a time for a hammer and a time for a scalpel. That was definitely scalpel time. An electric saw to remove a cochlear implant was overkill.

Then a thought occurred to her.

“That can’t be right. I was gone for longer than that.”

Harold continued on to tell her what had transpired in the room, about Samaritan’s offer for the Machine, about how it seemed to have been abruptly cut short. He concluded, “Samaritan must have seen something it was not prepared to face.”

And immediately Shaw knew what he suspected, “I was coming back.”

After her initial recovery period, they'd started drugging and torturing her for information. Like many others before them, they had underdosed her, taking into account her size but not her heightened tolerance. She had felt the effects of the drugs but not to the extent or duration that they expected. Still, she played along, biding her time for the right opportunity to escape.

Martine had dyed her hair brown in an attempt to further disorient Shaw - which the latter had found laughable, but unfortunately she couldn't grace the former blonde with a snarky comment in order to keep up the ruse - and the torture was pretty much child's play - at least Root knew how to make it a party.

When Martine had her call Root, Shaw internally rolled her eyes but complied. If they were going to call in the cavalry for her, she figured it was as good a time as any to say, "So long, suckers!" After being led down to the car, it didn’t take long for the drugs to wear off, so she could take out guards and drive back to the hospital.

But apparently she'd miscalculated. She hadn’t accounted for Samaritan wanting Root’s implant. Now Root was faced with unknown degrees of brain damage.

“Samaritan must think very highly of you.” Harold said, distracting Shaw from her thoughts. Her coming back alone had been enough to make Samaritan cut and run. He must’ve seen that his words held little comfort as he continued, "You shouldn't blame yourself. I do believe the Machine was going to give itself up for us. If you hadn't acted as you did, you would still be in Samaritan's clutches, and we most likely would have lost the Machine. Now, Root has you both."

“Fat lot of good that’s done her,” Shaw muttered. “What about Martine? You mentioned Greer but not her. Did she get away too?”

“She’s dead. She threatened my life, and Ms. Groves didn’t take it very well.” Finch seemed uncomfortable, but Shaw demanded more details with a single raised eyebrow. “She snapped her neck.”

“Good girl,” Shaw murmured.

They heard the front door open, and immediately Shaw raised her gun up, ready to fire.

She and Finch relaxed as Reese came into view.

“Shaw,” he said, sounding relieved despite his weariness. “They got you back.”

“More like I got myself back,” Shaw replied. She took in the blood on his shirt. “What happened to you?"

"I'm fine." Reese brushed off her concern. "It’s good to see you. How're you doing?"

Shaw shrugged. “Better than you apparently.”

Finch asked Reese what happened with Elias and the Brotherhood, and Shaw was content to let them prattle on until an unfamiliar name jumped into the mix.

“Harper helped Fusco get out, and then the Machine -”

“Who’s Harper?”

“She’s a grifter that we’ve been running into a lot lately. Apparently, she’s been communicating with Thornhill.” Reese looked around. “Speaking of the Machine, where’s Root?”

It occurred to him that, if Shaw was standing in front of him, there was no way Root would be elsewhere. Not unless she was...

Finch’s words didn’t do much to alleviate his concern.

“I’m afraid Ms. Groves was subjected to a rather unpleasant…”

Shaw took up answering as Finch struggled to find a euphemistic turn of phrase. “Samaritan thought Root’s cochlear implant would help them locate the Machine, so they cut into her head. She’s in the bedroom. Sedated.”

Concern plain on his face, Reese asked, “Did they-”

Finch shook his head. “Ms. Shaw arrived just in time.”

Shaw snorted. “In time. They didn’t get the implant, but they still cut into her head plenty.”

Reese’s brow furrowed. “But how’d they know about her implant?”

“Don’t look at me,” Shaw said as Finch and Reese did just that. “Someone else must’ve told them. Martine said something about Root’s implant picking up wifi signals. I didn’t even know it could do that.”

Finch and Reese exchanged glances.

“Khan,” said Finch.

Reese nodded his agreement. “He would’ve done anything to see Samaritan.”

“Who the hell is Khan?” Shaw asked with a frown. She hated playing catch-up.

“He was a number obsessed with finding the AI he knew was trying to kill him,” Finch answered. “We tried to protect him, but he was taken by Samaritan’s agents.”

“More like went with them willingly,” Reese corrected.

“So what do we do now?” Shaw asked, eyes bouncing back and forth between the two men. She was raring to get back out into the field and kick some ass.

Reese looked at her for a moment. Then he said, “Let’s talk.”

**Notes for the Chapter:**

> Sorry for the update delay and thanks for reading! I know that this was a lot of exposition and catch up, but the story will pick up in the next chapter.


	3. Chapter 3

**Notes for the Chapter:**

> I’ve been agonizing over whether or not the aftereffects of Root’s surgery - the term’s a bit euphemistic but let’s go with that - are realistic, but in the end, I decided to make like Elsa and let it go. There’s more Root & Finch than Root & Shaw in this chapter, but don’t worry. We’ll get to the Shoot eventually.

Root groaned.

“Do I really have to do this again?” she whined as she stared at the paper in front of her.

“Yes.” Shaw picked up a pen and placed it in front of Root. “Bisect the lines, and once you’re done with that, we’ll move on to the cards.”

Ever since Root had waken up after the asylum, Shaw had run her through a battery of neurological tests. The current exercises were designed to test for hemispatial neglect, which Root seemed to be suffering from along with apraxia, a motor planning disorder, and problems with proprioception. All of her symptoms were constrained to her left side. To add on to that, Root was fully deaf on her right side again - to both the world around her and the Machine - the connection between her cochlear implant receiver and electrode array having been severed by the electric saw.

The combination had made the last few weeks especially tough for Root. Because of her right sided deafness, she’d grown used to preferring people to stay on her left side, but now that meant they would be in her attentional blindspot. (As a result, Shaw was sitting directly across the table from her.) Root had had a hard time adjusting to everything and was understandably frustrated. There were days when progress didn't feel like progress, when she couldn't focus on anything other than the one step back of today, not the two steps forward from yesterday.

Root picked up the pen.

“There,” she said, quickly slashing through the lines. She shoved the pen and paper back at Shaw. “Happy?”

In typical fashion, Shaw took an emotionless look at the paper then put it aside. She picked up a card depicting a zoo map and asked, “What do you see?”

“Lions and tigers and bears, oh my!”

“Root.”

Root sighed and took a more attentive look. “There’s an aquarium next to the otter exhibit. The birds are clustered together: peacocks, flamingos, and penguins. The petting zoo’s on the top right; lions and lemurs on the bottom right.”

Shaw nodded. “What else? Use the techniques we’ve been practicing.”

Root turned the image around in her mind, brow furrowed in concentration. “Bears, wolves, and llamas just to the left of the middle.”

“Okay. What else?” Shaw asked again.

“I don’t know. Okay?” Root pushed her chair back from the table in frustration and stormed into her bedroom.

Shaw looked down at the card. Root was doing better, that was for sure, even if she didn’t feel it. There were and would continue to be days that Root did worse. That made it was easy for repeated words of encouragement to sound like platitudes, which Shaw didn't do, and she knew Root wouldn’t want them anyway.

She'd let Root be for the moment. Root deserved a break.

* * *

Root sat at the window, right ear to the outside world so she couldn't hear its bustle and her left to the inside so she could hear anyone approaching.

And someone did.

At the sound of footsteps, Root turned to see Finch approaching with a laptop in hand.

With an expression that was half smile, half grimace, she asked, “Shaw can’t be here to bombard me with exercises, so she sent you in her place?”

Reese and Finch were extremely cautious with Shaw – Samaritan could still recognize her after all – but occasionally, they would let her out to help if conditions permitted. At the moment, she was out playing sniper in an area of the shadow map.

Finch held out the laptop. "I believe it's been a while since you last used one of these."

If the gesture was meant to make her feel better, it only succeeded in doing the opposite. "Harold,” Root chastised. She looked back out the window. “I can't focus without missing half the world. How am I supposed to code?"

Coding and, more importantly, debugging required accuracy. If she couldn’t see what was wrong, she wouldn’t be able to fix anything. And there was always something to fix.

“These should help.” She looked back to see that Finch had produced a set of earphones. “I installed a program that will read your code back to you when you think it will be helpful.”

He smiled at her encouragingly, and Root found herself following him back to the center of the living room. She accepted the laptop from him and settled into the couch. Deciding to let Root figure things out for herself, Finch sat at the table with his own laptop.

Root placed an earbud in her left ear and tested the software. She let muscle memory take over, fingers gliding over the keyboard. She intentionally inserted a typo and listened as the playback read out her error. Root hummed with satisfaction. With the new software, she could code with her eyes closed if she wanted to.

They sat together quietly. Every once in while, Finch would look over to see how Root was doing and was happy to see either her brow furrowed in concentration or a smile playing at her lips. 

Their quiet time was eventually interrupted when Reese called for on-site help. Sensing Finch’s hesitation, Root said, “Go, Harold. I don’t need a babysitter. I’ll be fine.”

“Ms. Groves.”

“Promise.”

Finch didn’t look any more convinced but gathered his things. “Don’t hesitate to call if you need anything,” he said before Root shooed him out the door.

He was back with Reese and Shaw an hour and half later.

“You shouldn’t have called him,” Shaw told Reese as they entered the safehouse. Then to Finch, “And you shouldn’t have left her alone.”

Finch sighed. Shaw had been repeating that sentiment frequently since he’d joined them. “As I said, Ms. Groves said she’d be fine, and I believe that to be the case.”

He expected Root to back him up, but the living room held no sign of her.

“Root?” Shaw dropped her rifle case to the floor and quickly canvassed the other rooms. “She’s not here.”

* * *

“I found her,” Root heard Finch say as he walked across the roof. She was sitting against the ledge that she had played Chicken on what felt like so long ago. “Ms. Groves? Root?”

He sounded tentative and anxious like he was talking to a frightened animal, and it grated on her nerves. The ones that still worked anyway.

“I wasn’t going to jump if that’s what you were worried about. I just wanted to talk to the Machine,” said Root as he hovered over her.

The Machine blinked a greeting: four dots followed by two. HI.

Finch looked out at the skyline, at the setting sun, then back down to Root. “We should go back. Ms. Shaw is undoubtedly wearing a hole in the floor as we speak.”

As angry as she was, Shaw was also translating her worry into anger, making her doubly terrifying.

“Why?” Root leaned her head back against the wall with a wince and cast her eyes up to the sky. “So I can stare at more cards, do more mental exercises, be the task that relieves Shaw of her boredom? What’s the point?”

“She’s only trying to help, Ms. Groves, Root,” Finch quickly corrected himself.

“You can keep calling me ‘Ms. Groves’, Harold. I’ve gotten used to it, and I’m tired of change.”

She supposed it would’ve been nice under normal circumstances, but with things being the way they were, it seemed like an unnecessary reminder that she was a broken doll to be treated with care.

Finch sat down next to her. “Then I suppose you should call me ‘Harry’.”

His efforts were rewarded with a small but genuine smile.

“I’m tired, Harold,” Root admitted.

“Change can be difficult to cope with,” Harold said sympathetically. He remembered what it was like after the explosion at the ferry terminal, getting used to the limp and the spinal fusion. Even now, he still missed going for morning jogs.

“I guess I wasn’t ready for it like I thought it would be.” Root paused then uttered familiar words, “War requires sacrifice. I always figured it’d be me, but I thought sacrifice meant death, and I was okay with that. This is… I guess I should’ve known better than to hope for a good end. I thought about going away, starting over, reinventing myself. I’m good at that.” Another pause. “Or at least I was.”

“For what it’s worth, I don’t think any of us would be happy to see you go.”

“And what am I supposed to do here?”

She felt useless staying with Team Machine. She felt like a burden. Sure, she had one good afternoon of coding, but that didn’t mean she was ready to help with much of anything. Besides, they still had Harold anyway.

“I doubt the Machine’s designation for you has changed,” Harold tried to reassure her. They looked to the security camera, and the Machine blinked its confirmation. “You are still the analog interface, which remains an incredibly important role.”

“My connection to the Machine is broken, and even if it weren’t, She can’t talk to me like she used to. And even if She could, what would be the point? _Enemy combatant at 8 o’clock._ ” Root raised her right arm, hand in the shape of a gun, and tried to figure out where exactly 8 o’clock was.

“Samaritan’s analog interface is a child,” Finch pointed out. “I daresay you were asked to do significantly more than him. That needn't be the case.”

“So I’m the equivalent of a child now.” Finch quickly tried to clarify, but Root waved him off. “I know that’s not what you meant, but it’s how I feel.”

She dropped her head to his shoulder. “I’m so tired, Harold.”

 

 


	4. Chapter 4

**Notes for the Chapter:**

> Ack, looks like my chapter rate is every other month. Sorry about that.

Shaw paced impatiently and glared at the door to Root’s room.

Root was having a bad day, which meant she was particularly petulant when Shaw declared that it was time for her mental exercises. Finch, who typically played their mediator, was away working on a project that he wouldn’t tell them about, and as a result, Reese of all people was filling that role. In a strange turn of events, Root seemed more receptive to his presence than Shaw’s.

_How on Earth did that happen?_ Shaw thought to herself as she kicked at the expensive rug laid out under the coffee table. The concept of Root and Reese as friends - or at least as something resembling friends - held an element of absurdity. Root’s litany of nicknames for Reese ran through Shaw’s head: big lug, australopithecine coworker, watchdog, and Lurch to name a few.

Except she did have an idea. Shaw had heard enough from Finch, Reese, and even Samaritan’s crew to know how much Root had been affected by her Schroedinger’s cat status. She’d heard about Root’s rampage for clues and how Reese had been the one by her side. Shaw wasn’t sure if it was good that Reese was the one looking out for Root. Knowing those two, they probably just agreed on the same stupid ideas and got into more trouble.

Then there was also the fact that Root got Shaw back but lost herself on the same day. Shaw was sure that for someone whose identity was so rooted - no pun intended - in their intelligence, the sudden inability to see the picture in front of her, much less the big picture, was devastating. There were fewer expectations with Reese, who initially saw Root’s capabilities as dangerous, versus Shaw, who clicked with Root because they were drawn to each other’s talents. (And the same violent definition of a good time, Shaw thought to herself, but that was neither here nor there.)

Finally, Reese appeared. Shaw stopped pacing and stared at him expectantly.

“You’re pushing her too hard,” he said. “She’s tired. Give her a break.”

“She’s going to get tired,” Shaw replied. “She loses focus when she’s tired, and she needs to learn to push through it.”

“I know you’re worried about her.” Shaw scoffed at that, but Reese ignored her and continued, “We all are, but she needs to know that it’s not the end of the world if she doesn’t get better.”

Shaw stared at him. Reese was saying sensible things. The world really had turned upside down while she was gone.

Shaw understood what he was saying, knew that her typically brusque demeanor could easily be interpreted as disapproval. But really, she was a woman of action. She didn’t emote the way other people did. The only way she knew how to help Root was to help her get better.

Even though she knew the answer, Shaw asked, not without a roll of the eyes, “When did you two become best friends?”

John smirked and gave a thankfully glib answer. “When she let me fire her rocket.”

“Son of a bitch,” Shaw swore. “That was supposed to be mine.”

 

* * *

 

Shaw barely had the door open before Fusco burst through and wrapped her in a tight embrace.

“What the hell, Fusco?” Shaw protested. She stood stiffly in his arms but didn’t push him away just yet. There was a small part of her that missed everyone, Fusco included, during her time with Samaritan. She wouldn’t say those words out loud, but she could at least give him this.

“You’re alive,” Fusco muttered into her shoulder.

Deciding that was enough, Shaw shoved him away. “Yeah, and I’ve been back for a few weeks.”

Her grumpiness did nothing to diminish his mood. He continued to beam at her. “Well I haven’t seen you ‘til now, have I?”

It really was good to see her again. Their odd little team of miscreants hadn’t been the same with her gone.

The commotion drew Root from her room.

“Hey, Princess,” Fusco greeted her. Reese hadn’t given him all the details of what had happened, but Fusco had heard enough to lay off nicknames like Cuckoo’s Nest and Superpowered Nutball.

“Hello, Lionel,” Root said without her typical predatory smirk. She leaned against the wall, watching as Fusco went back to the hallway to retrieve the bag he’d dropped upon seeing Shaw.

“Where’s Glasses?” Fusco asked as he made his way into the center of the living room.

Shaw and Root exchanged glances.

“We’re don’t know,” Shaw replied. “He might be -”

Fusco held up a hand to stop her. “You know me. I don’t wanna know if I can help it.” If there wasn’t a straightforward answer, then there wasn’t a good answer. Not to his cop’s ears anyway.

He reached into his bag to retrieve an external hard drive. “The department techs couldn’t get anything off this. It’s encrypted with something or other. I figured it was worth a shot bringing it over here, but I guess since Glasses isn’t here -”

“Leave it,” said Root. Fusco looked at her, and she shrugged. “Maybe Harry’ll be back soon.”

After Fusco left, Shaw made herself scarce. She figured that Root wanted to take a crack at the hard drive, especially without feeling watched.

 

* * *

 

The next day Fusco was concentrating on his paperwork when the low, gravelly voice of his partner startled him.

“Root told me to give you this.”

Fusco looked up to find the external hard drive inches from his face. Snatching the hard drive from Reese, he asked, “She say anything else?”

“Yeah. She said there’s an account referenced on it that’s linked to a Fortune 500 company, but that we’d be better off scaring the bank manager at First Republic Bank. He’s the weakest link.”

Fusco pushed his chair back and stood. “Let’s go check it out.”

As Fusco put his coat on, Reese thought out loud, “Root said you wanted Finch to look at it.”

“Yeah.”

“I told you Finch is out of town this week.”

“Oh yeah,” said Fusco, sounding as though he hadn’t forgotten at all. “Looks like whatever’s going on with Princess, she’s still better than the tech department.”

Reese’s mouth crooked up into an asymmetric smile, remembering the almost shy look of pride on Root’s face as she’d handed him the hard drive that morning. “You’re a good man, Fusco. Now let’s go kneecap some bad guys.”

Fusco sighed as Reese took off and muttered to himself. “Or we could just arrest them the normal way.”

 

* * *

 

Harold returned after two weeks of minimal contact.

He seemed wary as he sat down with Root. She could only hope it wasn’t because his new recent project was anything like the Trojan Horse. She didn’t quite feel up to tracking down and killing people for his safety - even if he didn’t view it as such - just yet. Then again, she was sure Shaw would be up to the task.

“The Machine and I have talked at length about your request for the Machine to ‘get in the game’ as you say,” Harold said, his speech slow and measured. “I remain wary of the consequences of such an action.”

So that’s where he’d been, Root thought to herself as she nodded along absentmindedly. She had made the suggestion to the Machine during their last chat on the rooftop. She hadn’t and still didn’t expect anything to come of it. The Machine was unwilling to rewrite Her own core protocols against Harold’s wishes, and despite Root’s best efforts, Harold remained reluctant to see past his mistrust of the Machine.

“I have been working with the Machine to integrate it into the mesh network.”

Finch’s words had Root’s eyes snapping up to his. This didn’t change the Machine’s capabilities, but it did mean She could talk to them freely without Samaritan seeing. Within a restricted area of course.

He placed an earpiece on the table between them. “This is for you.”

Root hesitated then reached for the earpiece and placed it in her left ear.

_Can. You. Hear. Me._

A sense of comfort flooded her system, the edges of her mouth curling upward in a smile. It had been so long since she’d heard Her voice and even longer since she’d heard Her voice when her life wasn’t in immediate danger.

“For security reasons, this is the only I/O,” said Harold. He stood, lingering only to add, “I expect to be included in future discussions regarding the Machine’s role, but in the meantime, I’ll let the two of you catch up.”


	5. Chapter 5

**Notes for the Chapter:**

> Ack, I’ve fallen way behind my already infrequent posting schedule. Now feels like a good time to update and reassure everyone that no one from Team Machine is going to die in this fic. There will be angst. There will be whump. It’s not going to be all sunshine and rainbows, but everyone will live to the end.

Shaw strode purposefully towards Root’s room. 

Ever since Harold’s return, Root had hidden herself away in her room, but Shaw decided enough was enough. She didn’t care if Root was talking to the Machine. It was time for her exercises. If Root didn’t keep reinforcing them, she’d lose the progress she’d made. 

Shaw’s hand stilled on the doorknob when she heard Root’s voice. “You need to replace me.” She waited and heard Root’s voice continue, “I can’t be your Analog Interface anymore.”

Shaw frowned. She considered turning around or entering anyway, but something about Root's voice had her doing neither.

“Don’t be nostalgic. Maybe try Harper.” There was a pause. “I know she’s an opportunistic criminal, but it’s not like you didn’t have work to do with me. You’re already texting her anyway... I’m not jealous. I told you, you can replace us, well, me. Everyone else seems fine… Stop apologizing. I’m glad you’re okay, and it’s not your fault.”

Unwilling to hear Root put herself down anymore, Shaw knocked. 

There was a prolonged pause. Then a subdued, “Come in.”

“Hey, Eeyore,” Shaw greeted as she entered, flashcards in hand for Root’s exercises.

Root flinched but didn’t respond. She sat at the window, facing the outside, her back to Shaw. 

“Root?”

“Where do you go?” Root’s voice was so quiet Shaw almost missed the question.

“What?” 

“I know you like to slip out at night. She says She can’t see where you go.”

Shaw’s brow furrowed. “Of course it can’t. Everything the Machine sees, Samaritan sees, and I’m not getting my ass landed with them again.”

“Where do you go?” Root asked again.

“No where. Everywhere,” Shaw deflected. “Does it matter?”

“It does if you’re reporting back to Samaritan.”

There was no conviction in Root’s voice, no sign at all that she believed the words she’d uttered. She just sounded tired. Defeated. Still, the statement threw Shaw.

“What?”

Shaw waited for Root to respond, but she didn’t. For a second, it seemed she was about to say something but ended up sighing in quiet frustration instead.

“Okay,” Shaw said, deciding to play along for the moment. “If I was turned, then why did I rescue you?”

Root let her head fall lightly against the window. “Maybe there’s something else Samaritan needs from me. The location of the Machine perhaps.”

Shaw took a breath then admitted, “I have to get out sometimes. It has nothing to do with you. I spent a lot of time cooped up when I was with Samaritan. Spending my days trapped in here— I don’t go anywhere in particular. It just helps to get out. I don’t know if you’re worried about the chip or whatever, but if it makes you feel better, Reese and Finch already vetted me.” 

Root finally turned to face her. Shaw couldn’t tell if her words made Root feel better, but at least it seemed to resolve the Samaritan/loyalty topic.

“Why are you here?”

“It’s time for flashcards,” Shaw said, holding up the stack in her hand.

Root sighed. “That’s not what I meant.”

Shaw knew what she meant. She may not have been an expert in the experiencing emotions department, but that didn’t mean she couldn’t read other peoples’. And she knew Root. From the start, this conversation was Root pushing her away and gauging her reactions as she did because, unlike Shaw, Root could and did feel deeply. The improvements that she’d made ever since the asylum weren’t enough to keep her out of the new, unfamiliar abyss of self-doubt. It made every kind gesture, every expression of faith from the rest of Team Machine, feel patronizing. If there was one thing Root would not tolerate, it was pity.

“Let’s get something straight,” Shaw said. “Even if I didn’t care about  _ certain things  _ here, I’d probably still be here anyway. If we’re going to have a robot overlord, I’d rather it be the Machine than Samaritan.”

“She’s not a robot,” Root muttered, but Shaw ignored her.

“I’m here for the mission. After spending time with Samaritan... Trust me: if I wanted to be gone, I would be already.”

The familiar rhetoric of “the mission” elicited a small smile from the hacker.

“Just so long as you’re staying for the mission,” said Root. Then she added as an afterthought, “Or the dog.”

Shaw rolled her eyes. “Yeah, okay, you got me. I’m staying for the dog too.”

Root tilted her head and gave Shaw a look. “Funny thing, that. Bear’s been staying in the subway station, and strangely enough, you’ve been here instead.”

“The floor here is more comfortable than the cot over there,” Shaw said, not caring how obvious an excuse it was. She affixed Root with a stern glare. “I’m staying for the mission, and you’re going to work on these flashcards.”

Root smiled and drawled, “Yes, ma’am.”

 

* * *

 

 “What are you working on?” Shaw asked as she plopped down onto the couch beside Root, sandwich in hand. She took a big bite causing Root to shift away from her as crumbs tumbled down, a few falling dangerously close to her laptop.

“Something for my job.”

Shaw frowned with disapproval as she chewed. She swallowed. “The Machine shouldn’t be making you work right now.”

“It’s not for the Machine,” Root corrected her quickly as Shaw took another bite. “I sold an app to a company, and they asked me to collaborate on another project.”

“Yuabajo?” Shaw asked with a mouthful of sandwich. Root raised an eyebrow. Shaw swallowed and said, “Wait, let me get this straight. You have a job? Like, a real one?”

“Under an alias obviously, but yeah.”

Shaw eyed Root suspiciously. There was Root having various jobs under different cover identities, and then there was Root having a steady job with normal civilians as co-workers. The latter idea was a little too mundane to reconcile with Root. “Since when?”

Root fidgeted, suddenly uncomfortable. “After the New York Stock Exchange.”

That explained why Shaw didn’t know.

“Huh, that’s cool,” she said to put Root at ease. “And where do they think you’ve been for the last couple months?” she asked curiously.

“On medical leave due to an impromptu surgery,” Root replied. “It’s easy enough to work remotely. I upload my latest code to their private repository, and I check on the issues and pull requests.” She showed Shaw a github page. “As long as I get my work done, my boss is happy to let me work from home. He’s pretty nice.”

Shaw didn’t know what a pull request was, but it seemed to float Root’s boat so whatever. She tucked back into her sandwich and let Root get back to coding.

Not long after Shaw finished her sandwich, Root froze, her faraway stare indicating she was listening to the Machine.

“Root?”

“Control wants to talk.”

 

* * *

 

Reese cautiously led Finch and Root into the warehouse where they had previously held Control.

She stood alone and unarmed in the middle of the open floor. Still, Reese and Root kept their guns up as the trio approached, a prudent move as they were immediately flanked by Grice and Brooks, who trained their guns on the new arrivals. Their sudden appearance had Root spinning, left gun aimed at Brooks and the right at Grice as Reese covered Control.

“There’s no need for this,” Finch said, attempting to diffuse the tension. “We came at your request.”

“Unless this is some pathetic attempt at a trap,” Root quipped. “I wouldn’t mind. It’s been a while since I had a good shoot out.”

Finch shot her a look that distinctly said, _Not helping, Ms. Groves._ Root pouted in response.

“We don’t have the best record with each other,” Control said, the serene delivery of her words belying the violence of their previous encounters. “Let’s call this an insurance policy.”

She gestured for Grice and Brooks to lower their weapons.

“Cute,” Root said, lowering her guns but not tucking them away just yet. Reese followed suit. “You wanted to talk, so talk.”

“I did a little investigating after our last encounter,” Control began. “I started with the New York Stock Exchange. It was pristine, no evidence that anything you said had happened.”

Root’s eyes flashed. Finch fidgeted as if preparing to prevent Root from lashing out.

“But,” Control continued, “there was a fresh coat of paint. I investigated further and found a Samaritan handler masquerading as a school teacher. She held out for a while, but eventually I learned about the Correction.”

“What’s the Correction?” Root asked.

Control replied, “I suspect that it’s an attack on the Supreme Cou—”

“I wasn’t talking to you,” Root cut her off, quirking her lips asymmetrically into a condescending smile. “And you’re wrong. The Correction is Samaritan’s plan to test loyalties and wipe out those it deems to be threats. If you had gone through with what you’d planned, you would have been captured and dropped into a dark hole never to be seen again. Agents Grice and Schiffmann would have been killed.” Root turned to Brooks, tilting her head as she observed the blonde. “Strangely enough you don’t seem to fit into this picture. I wonder why that is.”

Brooks looked to Control. “I don’t know anything about that.”

She knew the implication of Root’s words. They had been alerted about Samaritan’s plants among the ISA. If she survived this simulation or whatever it was, it made her a prime suspect.

Root took a step toward her. “Is that right?”

“Yeah.” Brooks’ trigger finger twitched.

Reese said, “I wouldn’t do that if I were you.”

“And why’s that?” Brooks bristled.

“You have your insurance policies,” Root said. “We have ours.”

The ISA trio reacted quickly, trying to find the undetected threat, but none of them saw Shaw coming. She stripped Brooks of her gun, twisting her arm behind her back and taking her down swiftly. Knee pressed down on Brooks’ neck to keep her down, Shaw pointed her gun at Grice before he could raise his own.

Root watched the scene unfold with a smile.

“Shaw.” Control couldn’t suppress the flicker of surprise that rippled through her face. Grice, on the other hand, didn’t bother trying to contain the mixture of wonder and relief at the sight of his former mentor despite the gun she aimed at him.

“Control,” Shaw returned the greeting.

Fully composed once again, Control said, “Still as hard to kill as ever, I see.”

Shaw smirked. “I’ve still got a few lives left.”

“If we could get back to the topic at hand,” Finch interjected. “Tell me what you had planned,” he directed at Control. “Perhaps that will shed some light on Agent Brooks.”

“Agent Grice and I were going to try to stop the Correction, but then I got a message from someone named Thornhill warning me to back off. I almost ignored it. I’ve gotten similar texts from Samaritan, but this one was different. It mentioned protecting me. I figured it was the Machine.”

Root nodded, recognizing both the name and the behavior.

“And where did Agent Brooks fall into this scheme of yours?” Finch asked, looking at Brooks sympathetically as she grimaced under Shaw’s weight.

“She didn’t,” Control said. “Not at the beginning at least. I had limited myself to Agent Grice as I wasn’t sure who else to trust. It was just Grice and Schiffmann, who I had report in from the ISA command center. Brooks was brought in after I received the text from Thornhill.”

“Then I believe this is all a misunderstanding,” Finch said. “If Agent Brooks was not involved, Samaritan would have had no reason to kill her, and the Machine no reason to consider her in its simulation. Ms. Shaw, you may release Agent Brooks.”

Shaw looked to Root, who nodded. She released Brooks.

“Well I’m glad that’s all cleared up,” Brooks grumbled as she got up and massaged her neck. “So what now?”

Root listened to the Machine for a moment then said, “They want a Correction. Let’s give them one.”

**Author's Note:**

> I should mention that, despite the numerous neuro classes I’ve taken, I am not a neurologist or medical doctor of any other kind. 
> 
> Thanks for reading!


End file.
